Variant rs208870 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.93 in 152,240 control chromosomes in the GnomAD database, including 66,042 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.93 ( 66042 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.995

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.930

AC:

141546

AN:

152122

Hom.:

65991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.880

Gnomad AMI

AF:

0.992

Gnomad AMR

AF:

0.950

Gnomad ASJ

AF:

0.956

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.960

Gnomad FIN

AF:

0.937

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.947

Gnomad OTH

AF:

0.918

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.930

AC:

141656

AN:

152240

Hom.:

66042

Cov.:

AF XY:

0.930

AC XY:

69227

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.880

Gnomad4 AMR

AF:

0.950

Gnomad4 ASJ

AF:

0.956

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.960

Gnomad4 FIN

AF:

0.937

Gnomad4 NFE

AF:

0.947

Gnomad4 OTH

AF:

0.919

Alfa

AF:

0.942

Hom.:

30531

Bravo

AF:

0.930

Asia WGS

AF:

0.972

AC:

3380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.15

DANN

Benign

0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over